Starting phenix.real_space_refine on Thu Jul 24 09:52:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rxh_24731/07_2025/7rxh_24731_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rxh_24731/07_2025/7rxh_24731.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7rxh_24731/07_2025/7rxh_24731.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rxh_24731/07_2025/7rxh_24731.map" model { file = "/net/cci-nas-00/data/ceres_data/7rxh_24731/07_2025/7rxh_24731_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rxh_24731/07_2025/7rxh_24731_neut.cif" } resolution = 2.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Ca 2 9.91 5 P 15 5.49 5 S 18 5.16 5 C 3653 2.51 5 N 849 2.21 5 O 1046 1.98 5 H 48 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 5631 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5062 Number of conformers: 1 Conformer: "" Number of residues, atoms: 626, 5062 Classifications: {'peptide': 626} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 30, 'TRANS': 595} Chain breaks: 1 Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 65 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 8, 'ARG:plan': 1, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 52 Chain: "A" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 569 Unusual residues: {' CA': 2, 'PGW': 16} Classifications: {'undetermined': 18, 'water': 24} Link IDs: {None: 41} Unresolved non-hydrogen bonds: 321 Unresolved non-hydrogen angles: 338 Unresolved non-hydrogen dihedrals: 357 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'PGW:plan-2': 1, 'PGW:plan-3': 10} Unresolved non-hydrogen planarities: 37 Time building chain proxies: 4.25, per 1000 atoms: 0.75 Number of scatterers: 5631 At special positions: 0 Unit cell: (72.7901, 85.5107, 98.938, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 2 19.99 S 18 16.00 P 15 15.00 O 1046 8.00 N 849 7.00 C 3653 6.00 H 48 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.57 Conformation dependent library (CDL) restraints added in 764.9 milliseconds 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1200 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 3 sheets defined 73.3% alpha, 4.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'A' and resid 28 through 46 Processing helix chain 'A' and resid 68 through 86 Processing helix chain 'A' and resid 95 through 99 Processing helix chain 'A' and resid 103 through 117 Processing helix chain 'A' and resid 118 through 122 Processing helix chain 'A' and resid 144 through 156 Processing helix chain 'A' and resid 162 through 174 Processing helix chain 'A' and resid 174 through 191 Processing helix chain 'A' and resid 191 through 205 Processing helix chain 'A' and resid 209 through 238 Processing helix chain 'A' and resid 242 through 247 Processing helix chain 'A' and resid 272 through 281 Processing helix chain 'A' and resid 282 through 311 Processing helix chain 'A' and resid 317 through 350 removed outlier: 4.462A pdb=" N ILE A 323 " --> pdb=" O TYR A 319 " (cutoff:3.500A) Proline residue: A 324 - end of helix Proline residue: A 333 - end of helix Processing helix chain 'A' and resid 354 through 384 removed outlier: 3.980A pdb=" N VAL A 368 " --> pdb=" O GLN A 364 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N VAL A 369 " --> pdb=" O LYS A 365 " (cutoff:3.500A) Proline residue: A 377 - end of helix Processing helix chain 'A' and resid 392 through 398 removed outlier: 4.124A pdb=" N ASP A 397 " --> pdb=" O PRO A 394 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N VAL A 398 " --> pdb=" O TYR A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 404 removed outlier: 4.336A pdb=" N VAL A 403 " --> pdb=" O PHE A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 414 Processing helix chain 'A' and resid 424 through 435 Processing helix chain 'A' and resid 435 through 463 removed outlier: 4.735A pdb=" N VAL A 448 " --> pdb=" O LEU A 444 " (cutoff:3.500A) Proline residue: A 449 - end of helix Processing helix chain 'A' and resid 490 through 501 Processing helix chain 'A' and resid 507 through 526 removed outlier: 4.054A pdb=" N ASP A 511 " --> pdb=" O ASP A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 529 No H-bonds generated for 'chain 'A' and resid 527 through 529' Processing helix chain 'A' and resid 531 through 554 removed outlier: 3.787A pdb=" N ARG A 545 " --> pdb=" O TRP A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 591 removed outlier: 4.419A pdb=" N ASP A 571 " --> pdb=" O GLY A 567 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE A 582 " --> pdb=" O TRP A 578 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N SER A 585 " --> pdb=" O SER A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 634 removed outlier: 3.528A pdb=" N LYS A 634 " --> pdb=" O SER A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 658 Processing sheet with id=AA1, first strand: chain 'A' and resid 48 through 54 removed outlier: 3.764A pdb=" N ALA A 138 " --> pdb=" O ARG A 21 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ASN A 23 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N VAL A 136 " --> pdb=" O ASN A 23 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 260 through 261 removed outlier: 4.119A pdb=" N GLU A 266 " --> pdb=" O ASP A 261 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 504 through 505 removed outlier: 6.672A pdb=" N GLU A 504 " --> pdb=" O LYS A 556 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 347 hydrogen bonds defined for protein. 1011 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.49 Time building geometry restraints manager: 1.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 48 1.03 - 1.22: 33 1.22 - 1.42: 2317 1.42 - 1.61: 3274 1.61 - 1.81: 52 Bond restraints: 5724 Sorted by residual: bond pdb=" C1 PGW A 810 " pdb=" O01 PGW A 810 " ideal model delta sigma weight residual 1.332 1.426 -0.094 2.00e-02 2.50e+03 2.22e+01 bond pdb=" C1 PGW A 807 " pdb=" O01 PGW A 807 " ideal model delta sigma weight residual 1.332 1.422 -0.090 2.00e-02 2.50e+03 2.02e+01 bond pdb=" C1 PGW A 809 " pdb=" O01 PGW A 809 " ideal model delta sigma weight residual 1.332 1.422 -0.090 2.00e-02 2.50e+03 2.02e+01 bond pdb=" C1 PGW A 817 " pdb=" O01 PGW A 817 " ideal model delta sigma weight residual 1.332 1.421 -0.089 2.00e-02 2.50e+03 1.96e+01 bond pdb=" C1 PGW A 814 " pdb=" O01 PGW A 814 " ideal model delta sigma weight residual 1.332 1.420 -0.088 2.00e-02 2.50e+03 1.93e+01 ... (remaining 5719 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.29: 7127 2.29 - 4.58: 342 4.58 - 6.87: 124 6.87 - 9.16: 20 9.16 - 11.45: 39 Bond angle restraints: 7652 Sorted by residual: angle pdb=" N ARG A 404 " pdb=" CA ARG A 404 " pdb=" C ARG A 404 " ideal model delta sigma weight residual 113.16 119.81 -6.65 1.42e+00 4.96e-01 2.19e+01 angle pdb=" N GLU A 418 " pdb=" CA GLU A 418 " pdb=" C GLU A 418 " ideal model delta sigma weight residual 109.96 103.92 6.04 1.50e+00 4.44e-01 1.62e+01 angle pdb=" C ARG A 404 " pdb=" N PRO A 405 " pdb=" CA PRO A 405 " ideal model delta sigma weight residual 119.84 114.93 4.91 1.25e+00 6.40e-01 1.54e+01 angle pdb=" O11 PGW A 807 " pdb=" P PGW A 807 " pdb=" O12 PGW A 807 " ideal model delta sigma weight residual 98.90 110.35 -11.45 3.00e+00 1.11e-01 1.46e+01 angle pdb=" N ILE A 421 " pdb=" CA ILE A 421 " pdb=" C ILE A 421 " ideal model delta sigma weight residual 109.51 114.97 -5.46 1.43e+00 4.89e-01 1.46e+01 ... (remaining 7647 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.98: 3238 34.98 - 69.95: 182 69.95 - 104.93: 35 104.93 - 139.90: 8 139.90 - 174.87: 11 Dihedral angle restraints: 3474 sinusoidal: 1624 harmonic: 1850 Sorted by residual: dihedral pdb=" CA ALA A 389 " pdb=" C ALA A 389 " pdb=" N SER A 390 " pdb=" CA SER A 390 " ideal model delta harmonic sigma weight residual 180.00 153.91 26.09 0 5.00e+00 4.00e-02 2.72e+01 dihedral pdb=" O01 PGW A 810 " pdb=" C01 PGW A 810 " pdb=" C02 PGW A 810 " pdb=" O03 PGW A 810 " ideal model delta sinusoidal sigma weight residual 59.30 -115.57 174.87 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C03 PGW A 810 " pdb=" C01 PGW A 810 " pdb=" C02 PGW A 810 " pdb=" O03 PGW A 810 " ideal model delta sinusoidal sigma weight residual 295.35 121.86 173.49 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 3471 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 707 0.068 - 0.136: 88 0.136 - 0.203: 16 0.203 - 0.271: 0 0.271 - 0.339: 1 Chirality restraints: 812 Sorted by residual: chirality pdb=" CA ARG A 404 " pdb=" N ARG A 404 " pdb=" C ARG A 404 " pdb=" CB ARG A 404 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.87e+00 chirality pdb=" CA ILE A 421 " pdb=" N ILE A 421 " pdb=" C ILE A 421 " pdb=" CB ILE A 421 " both_signs ideal model delta sigma weight residual False 2.43 2.25 0.19 2.00e-01 2.50e+01 8.65e-01 chirality pdb=" C02 PGW A 813 " pdb=" C01 PGW A 813 " pdb=" C03 PGW A 813 " pdb=" O01 PGW A 813 " both_signs ideal model delta sigma weight residual False 2.36 2.54 -0.18 2.00e-01 2.50e+01 8.11e-01 ... (remaining 809 not shown) Planarity restraints: 930 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR A 352 " -0.010 2.00e-02 2.50e+03 1.92e-02 3.70e+00 pdb=" C TYR A 352 " 0.033 2.00e-02 2.50e+03 pdb=" O TYR A 352 " -0.013 2.00e-02 2.50e+03 pdb=" N GLU A 353 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 393 " 0.030 5.00e-02 4.00e+02 4.52e-02 3.26e+00 pdb=" N PRO A 394 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO A 394 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 394 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 526 " 0.029 5.00e-02 4.00e+02 4.32e-02 2.98e+00 pdb=" N PRO A 527 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO A 527 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 527 " 0.024 5.00e-02 4.00e+02 ... (remaining 927 not shown) Histogram of nonbonded interaction distances: 1.72 - 2.30: 30 2.30 - 2.87: 2026 2.87 - 3.45: 6618 3.45 - 4.02: 11498 4.02 - 4.60: 16821 Nonbonded interactions: 36993 Sorted by model distance: nonbonded pdb=" OG SER A 546 " pdb=" H1 HOH A2702 " model vdw 1.723 2.450 nonbonded pdb=" O LYS A 556 " pdb=" H1 HOH A2709 " model vdw 1.739 2.450 nonbonded pdb=" OH TYR A 621 " pdb=" H1 HOH A2704 " model vdw 1.740 2.450 nonbonded pdb=" OG1 THR A 116 " pdb=" H1 HOH A2705 " model vdw 1.769 2.450 nonbonded pdb=" OD2 ASP A 233 " pdb=" H1 HOH A2703 " model vdw 1.778 2.450 ... (remaining 36988 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.160 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 17.660 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.094 5676 Z= 0.433 Angle : 1.403 11.447 7628 Z= 0.571 Chirality : 0.050 0.339 812 Planarity : 0.005 0.045 930 Dihedral : 24.726 174.875 2274 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.73 % Favored : 97.11 % Rotamer: Outliers : 0.56 % Allowed : 2.22 % Favored : 97.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.31), residues: 622 helix: 0.09 (0.22), residues: 424 sheet: -0.80 (0.80), residues: 27 loop : -2.04 (0.45), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP A 155 HIS 0.008 0.002 HIS A 619 PHE 0.018 0.002 PHE A 388 TYR 0.013 0.002 TYR A 352 ARG 0.005 0.001 ARG A 496 Details of bonding type rmsd hydrogen bonds : bond 0.10973 ( 347) hydrogen bonds : angle 5.47823 ( 1011) covalent geometry : bond 0.00872 ( 5676) covalent geometry : angle 1.40329 ( 7628) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 91 time to evaluate : 0.600 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 92 average time/residue: 1.2725 time to fit residues: 122.3897 Evaluate side-chains 51 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 50 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 421 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 52 optimal weight: 0.0970 chunk 46 optimal weight: 2.9990 chunk 26 optimal weight: 0.4980 chunk 16 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 7.9990 chunk 48 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 56 optimal weight: 0.6980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 78 GLN ** A 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 148 ASN A 171 ASN A 283 GLN A 370 ASN A 438 GLN A 453 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.104847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.075510 restraints weight = 8095.171| |-----------------------------------------------------------------------------| r_work (start): 0.2895 rms_B_bonded: 2.02 r_work: 0.2734 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.2591 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.2968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5676 Z= 0.143 Angle : 0.556 6.021 7628 Z= 0.278 Chirality : 0.038 0.156 812 Planarity : 0.004 0.034 930 Dihedral : 25.009 168.624 1100 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 15.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.67 % Allowed : 10.93 % Favored : 87.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.33), residues: 622 helix: 1.50 (0.24), residues: 426 sheet: -0.29 (0.89), residues: 27 loop : -1.52 (0.48), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 155 HIS 0.003 0.001 HIS A 400 PHE 0.009 0.001 PHE A 193 TYR 0.016 0.001 TYR A 180 ARG 0.005 0.001 ARG A 562 Details of bonding type rmsd hydrogen bonds : bond 0.04397 ( 347) hydrogen bonds : angle 4.29571 ( 1011) covalent geometry : bond 0.00299 ( 5676) covalent geometry : angle 0.55584 ( 7628) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 50 time to evaluate : 0.563 Fit side-chains REVERT: A 28 ASP cc_start: 0.7751 (t0) cc_final: 0.7045 (t0) REVERT: A 104 GLU cc_start: 0.8205 (mt-10) cc_final: 0.7862 (tt0) outliers start: 9 outliers final: 6 residues processed: 55 average time/residue: 1.2473 time to fit residues: 71.9535 Evaluate side-chains 50 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 44 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 353 GLU Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 592 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 53 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 2 optimal weight: 0.5980 chunk 51 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 49 optimal weight: 0.0770 overall best weight: 1.3342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 54 GLN A 113 HIS A 230 GLN A 539 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.096731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.067180 restraints weight = 8209.760| |-----------------------------------------------------------------------------| r_work (start): 0.2750 rms_B_bonded: 2.03 r_work: 0.2577 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.2431 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8766 moved from start: 0.5342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 5676 Z= 0.204 Angle : 0.527 5.832 7628 Z= 0.284 Chirality : 0.040 0.157 812 Planarity : 0.004 0.033 930 Dihedral : 21.653 174.689 1100 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.22 % Allowed : 10.93 % Favored : 86.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.34), residues: 622 helix: 1.96 (0.25), residues: 425 sheet: -0.06 (0.99), residues: 24 loop : -1.18 (0.47), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 155 HIS 0.007 0.001 HIS A 619 PHE 0.015 0.001 PHE A 193 TYR 0.017 0.002 TYR A 589 ARG 0.005 0.000 ARG A 642 Details of bonding type rmsd hydrogen bonds : bond 0.05318 ( 347) hydrogen bonds : angle 4.30183 ( 1011) covalent geometry : bond 0.00454 ( 5676) covalent geometry : angle 0.52727 ( 7628) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 42 time to evaluate : 0.603 Fit side-chains REVERT: A 28 ASP cc_start: 0.7889 (t0) cc_final: 0.7152 (t0) REVERT: A 104 GLU cc_start: 0.8570 (mt-10) cc_final: 0.8261 (tt0) REVERT: A 146 GLU cc_start: 0.8874 (OUTLIER) cc_final: 0.8653 (tp30) REVERT: A 211 ILE cc_start: 0.9113 (OUTLIER) cc_final: 0.8907 (tp) REVERT: A 592 SER cc_start: 0.8882 (OUTLIER) cc_final: 0.8654 (p) REVERT: A 647 ARG cc_start: 0.7497 (tpt170) cc_final: 0.7059 (ttp80) outliers start: 12 outliers final: 3 residues processed: 49 average time/residue: 1.2881 time to fit residues: 66.2830 Evaluate side-chains 41 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 35 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 GLU Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 454 ARG Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 658 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 42 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 32 optimal weight: 0.1980 chunk 50 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 49 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 135 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.096826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.067695 restraints weight = 8357.294| |-----------------------------------------------------------------------------| r_work (start): 0.2756 rms_B_bonded: 2.02 r_work: 0.2589 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.2446 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.5571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 5676 Z= 0.162 Angle : 0.460 4.709 7628 Z= 0.249 Chirality : 0.039 0.150 812 Planarity : 0.003 0.030 930 Dihedral : 19.823 179.775 1098 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.22 % Allowed : 9.63 % Favored : 88.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.35), residues: 622 helix: 2.32 (0.25), residues: 424 sheet: 0.78 (1.05), residues: 22 loop : -1.05 (0.48), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 155 HIS 0.005 0.001 HIS A 619 PHE 0.011 0.001 PHE A 193 TYR 0.011 0.001 TYR A 212 ARG 0.003 0.000 ARG A 268 Details of bonding type rmsd hydrogen bonds : bond 0.04597 ( 347) hydrogen bonds : angle 4.11447 ( 1011) covalent geometry : bond 0.00359 ( 5676) covalent geometry : angle 0.46025 ( 7628) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 44 time to evaluate : 0.561 Fit side-chains REVERT: A 26 ASP cc_start: 0.8670 (p0) cc_final: 0.8359 (p0) REVERT: A 28 ASP cc_start: 0.7876 (t0) cc_final: 0.7302 (t0) REVERT: A 56 ASP cc_start: 0.7835 (m-30) cc_final: 0.7582 (m-30) REVERT: A 104 GLU cc_start: 0.8485 (mt-10) cc_final: 0.8175 (tt0) REVERT: A 211 ILE cc_start: 0.9037 (OUTLIER) cc_final: 0.8765 (tp) REVERT: A 305 GLU cc_start: 0.8970 (tp30) cc_final: 0.8670 (tt0) REVERT: A 420 SER cc_start: 0.8075 (t) cc_final: 0.7613 (p) REVERT: A 454 ARG cc_start: 0.7942 (OUTLIER) cc_final: 0.7390 (tpt170) REVERT: A 647 ARG cc_start: 0.7468 (tpt170) cc_final: 0.7059 (ttp80) outliers start: 12 outliers final: 4 residues processed: 52 average time/residue: 1.3532 time to fit residues: 73.6727 Evaluate side-chains 46 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 40 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 353 GLU Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 454 ARG Chi-restraints excluded: chain A residue 611 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 38 optimal weight: 0.0040 chunk 6 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 overall best weight: 1.1396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.095877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.066613 restraints weight = 8199.509| |-----------------------------------------------------------------------------| r_work (start): 0.2742 rms_B_bonded: 2.01 r_work: 0.2575 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.2432 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.5832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5676 Z= 0.164 Angle : 0.452 5.171 7628 Z= 0.247 Chirality : 0.038 0.148 812 Planarity : 0.003 0.029 930 Dihedral : 18.318 176.691 1098 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.22 % Allowed : 10.37 % Favored : 87.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.17 (0.35), residues: 622 helix: 2.39 (0.25), residues: 423 sheet: 0.42 (1.06), residues: 24 loop : -0.85 (0.50), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 155 HIS 0.005 0.001 HIS A 619 PHE 0.011 0.001 PHE A 193 TYR 0.014 0.001 TYR A 212 ARG 0.004 0.000 ARG A 642 Details of bonding type rmsd hydrogen bonds : bond 0.04732 ( 347) hydrogen bonds : angle 4.11519 ( 1011) covalent geometry : bond 0.00366 ( 5676) covalent geometry : angle 0.45168 ( 7628) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 41 time to evaluate : 0.916 Fit side-chains REVERT: A 26 ASP cc_start: 0.8746 (p0) cc_final: 0.8459 (p0) REVERT: A 28 ASP cc_start: 0.8015 (t0) cc_final: 0.7606 (t0) REVERT: A 104 GLU cc_start: 0.8501 (mt-10) cc_final: 0.8181 (tt0) REVERT: A 211 ILE cc_start: 0.9050 (OUTLIER) cc_final: 0.8770 (tp) REVERT: A 305 GLU cc_start: 0.8933 (tp30) cc_final: 0.8723 (tt0) REVERT: A 454 ARG cc_start: 0.7990 (OUTLIER) cc_final: 0.7467 (tpt170) REVERT: A 647 ARG cc_start: 0.7508 (tpt170) cc_final: 0.7072 (ttp80) outliers start: 12 outliers final: 3 residues processed: 48 average time/residue: 1.4920 time to fit residues: 75.4107 Evaluate side-chains 41 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 36 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 454 ARG Chi-restraints excluded: chain A residue 611 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 50 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 27 optimal weight: 0.7980 chunk 55 optimal weight: 0.7980 chunk 48 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 185 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.096127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.066918 restraints weight = 8190.407| |-----------------------------------------------------------------------------| r_work (start): 0.2748 rms_B_bonded: 2.03 r_work: 0.2582 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.2439 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8768 moved from start: 0.5972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5676 Z= 0.152 Angle : 0.442 4.864 7628 Z= 0.241 Chirality : 0.038 0.145 812 Planarity : 0.003 0.028 930 Dihedral : 17.317 173.120 1098 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.22 % Allowed : 10.37 % Favored : 87.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.33 (0.36), residues: 622 helix: 2.50 (0.26), residues: 424 sheet: 0.59 (1.09), residues: 24 loop : -0.82 (0.50), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 155 HIS 0.005 0.001 HIS A 619 PHE 0.009 0.001 PHE A 193 TYR 0.010 0.001 TYR A 212 ARG 0.003 0.000 ARG A 268 Details of bonding type rmsd hydrogen bonds : bond 0.04522 ( 347) hydrogen bonds : angle 4.05110 ( 1011) covalent geometry : bond 0.00339 ( 5676) covalent geometry : angle 0.44205 ( 7628) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 41 time to evaluate : 0.686 Fit side-chains REVERT: A 26 ASP cc_start: 0.8826 (p0) cc_final: 0.8534 (p0) REVERT: A 28 ASP cc_start: 0.7990 (t0) cc_final: 0.7508 (t0) REVERT: A 104 GLU cc_start: 0.8480 (mt-10) cc_final: 0.8156 (tt0) REVERT: A 211 ILE cc_start: 0.9012 (OUTLIER) cc_final: 0.8734 (tp) REVERT: A 420 SER cc_start: 0.8042 (t) cc_final: 0.7605 (p) REVERT: A 454 ARG cc_start: 0.8024 (OUTLIER) cc_final: 0.7426 (tpt170) REVERT: A 647 ARG cc_start: 0.7499 (tpt170) cc_final: 0.7064 (ttp80) outliers start: 12 outliers final: 6 residues processed: 48 average time/residue: 1.9021 time to fit residues: 95.3589 Evaluate side-chains 49 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 41 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 GLU Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 353 GLU Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 454 ARG Chi-restraints excluded: chain A residue 611 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 33 optimal weight: 3.9990 chunk 14 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 39 optimal weight: 10.0000 chunk 43 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 24 optimal weight: 0.0870 chunk 20 optimal weight: 0.5980 overall best weight: 1.4962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 185 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.094553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.065536 restraints weight = 8299.732| |-----------------------------------------------------------------------------| r_work (start): 0.2713 rms_B_bonded: 2.02 r_work: 0.2544 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.2401 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8812 moved from start: 0.6087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 5676 Z= 0.200 Angle : 0.481 5.816 7628 Z= 0.263 Chirality : 0.040 0.158 812 Planarity : 0.003 0.027 930 Dihedral : 17.203 170.896 1098 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.22 % Allowed : 10.56 % Favored : 87.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.22 (0.35), residues: 622 helix: 2.39 (0.25), residues: 423 sheet: 0.60 (1.09), residues: 24 loop : -0.76 (0.51), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 155 HIS 0.006 0.001 HIS A 619 PHE 0.013 0.001 PHE A 193 TYR 0.015 0.001 TYR A 212 ARG 0.004 0.000 ARG A 268 Details of bonding type rmsd hydrogen bonds : bond 0.05038 ( 347) hydrogen bonds : angle 4.18512 ( 1011) covalent geometry : bond 0.00453 ( 5676) covalent geometry : angle 0.48150 ( 7628) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 44 time to evaluate : 0.559 Fit side-chains REVERT: A 28 ASP cc_start: 0.8114 (t0) cc_final: 0.7665 (t0) REVERT: A 104 GLU cc_start: 0.8546 (mt-10) cc_final: 0.8210 (tt0) REVERT: A 211 ILE cc_start: 0.9088 (OUTLIER) cc_final: 0.8820 (tp) REVERT: A 454 ARG cc_start: 0.8053 (OUTLIER) cc_final: 0.7552 (mmt-90) REVERT: A 647 ARG cc_start: 0.7498 (tpt170) cc_final: 0.7089 (ttp80) outliers start: 12 outliers final: 5 residues processed: 49 average time/residue: 1.3916 time to fit residues: 71.3234 Evaluate side-chains 47 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 40 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 GLU Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 454 ARG Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 659 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 46 optimal weight: 3.9990 chunk 18 optimal weight: 0.5980 chunk 53 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 185 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.093974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.065032 restraints weight = 8230.821| |-----------------------------------------------------------------------------| r_work (start): 0.2706 rms_B_bonded: 2.01 r_work: 0.2536 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2393 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8818 moved from start: 0.6216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 5676 Z= 0.221 Angle : 0.492 5.616 7628 Z= 0.269 Chirality : 0.040 0.161 812 Planarity : 0.003 0.027 930 Dihedral : 16.857 166.276 1098 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.04 % Allowed : 10.37 % Favored : 87.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.24 (0.35), residues: 622 helix: 2.42 (0.25), residues: 423 sheet: 0.57 (1.07), residues: 24 loop : -0.76 (0.52), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 155 HIS 0.006 0.001 HIS A 619 PHE 0.013 0.001 PHE A 193 TYR 0.014 0.001 TYR A 212 ARG 0.004 0.000 ARG A 268 Details of bonding type rmsd hydrogen bonds : bond 0.05123 ( 347) hydrogen bonds : angle 4.23357 ( 1011) covalent geometry : bond 0.00503 ( 5676) covalent geometry : angle 0.49210 ( 7628) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 44 time to evaluate : 0.571 Fit side-chains REVERT: A 26 ASP cc_start: 0.8940 (p0) cc_final: 0.8634 (p0) REVERT: A 28 ASP cc_start: 0.8166 (t0) cc_final: 0.7751 (t0) REVERT: A 104 GLU cc_start: 0.8577 (mt-10) cc_final: 0.8226 (tt0) REVERT: A 211 ILE cc_start: 0.9098 (OUTLIER) cc_final: 0.8833 (tp) REVERT: A 420 SER cc_start: 0.8328 (t) cc_final: 0.7875 (p) REVERT: A 454 ARG cc_start: 0.8105 (OUTLIER) cc_final: 0.7623 (mmt-90) REVERT: A 647 ARG cc_start: 0.7483 (tpt170) cc_final: 0.7064 (ttp80) outliers start: 11 outliers final: 5 residues processed: 51 average time/residue: 1.4349 time to fit residues: 76.5276 Evaluate side-chains 47 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 40 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 GLU Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 353 GLU Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 454 ARG Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 659 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 49 optimal weight: 0.6980 chunk 9 optimal weight: 0.5980 chunk 35 optimal weight: 0.6980 chunk 36 optimal weight: 0.5980 chunk 13 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 25 optimal weight: 0.4980 chunk 28 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 185 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.096896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.067807 restraints weight = 8240.968| |-----------------------------------------------------------------------------| r_work (start): 0.2767 rms_B_bonded: 2.04 r_work: 0.2596 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.2453 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.6265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5676 Z= 0.116 Angle : 0.415 6.095 7628 Z= 0.225 Chirality : 0.037 0.136 812 Planarity : 0.003 0.027 930 Dihedral : 15.656 157.346 1098 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.11 % Allowed : 11.30 % Favored : 87.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.47 (0.36), residues: 622 helix: 2.61 (0.26), residues: 425 sheet: 0.70 (1.10), residues: 24 loop : -0.78 (0.52), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 155 HIS 0.004 0.000 HIS A 619 PHE 0.005 0.001 PHE A 525 TYR 0.010 0.001 TYR A 180 ARG 0.004 0.000 ARG A 268 Details of bonding type rmsd hydrogen bonds : bond 0.04117 ( 347) hydrogen bonds : angle 3.99691 ( 1011) covalent geometry : bond 0.00251 ( 5676) covalent geometry : angle 0.41475 ( 7628) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 45 time to evaluate : 0.562 Fit side-chains REVERT: A 26 ASP cc_start: 0.8915 (p0) cc_final: 0.8608 (p0) REVERT: A 28 ASP cc_start: 0.8095 (t0) cc_final: 0.7688 (t0) REVERT: A 104 GLU cc_start: 0.8481 (mt-10) cc_final: 0.8134 (tt0) REVERT: A 129 ARG cc_start: 0.8815 (mtt90) cc_final: 0.8577 (mtt90) REVERT: A 211 ILE cc_start: 0.8984 (OUTLIER) cc_final: 0.8670 (tp) REVERT: A 420 SER cc_start: 0.8092 (t) cc_final: 0.7658 (p) REVERT: A 454 ARG cc_start: 0.8087 (OUTLIER) cc_final: 0.7602 (mmt-90) REVERT: A 647 ARG cc_start: 0.7490 (tpt170) cc_final: 0.7059 (ttp80) outliers start: 6 outliers final: 1 residues processed: 48 average time/residue: 1.4942 time to fit residues: 74.8959 Evaluate side-chains 45 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 42 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 454 ARG Chi-restraints excluded: chain A residue 611 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 47 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 18 optimal weight: 0.5980 chunk 30 optimal weight: 4.9990 chunk 13 optimal weight: 0.0170 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 185 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.097224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.068390 restraints weight = 8325.829| |-----------------------------------------------------------------------------| r_work (start): 0.2775 rms_B_bonded: 2.04 r_work: 0.2607 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.2466 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 0.6319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 5676 Z= 0.113 Angle : 0.422 6.113 7628 Z= 0.228 Chirality : 0.037 0.136 812 Planarity : 0.003 0.027 930 Dihedral : 14.726 147.409 1098 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 0.93 % Allowed : 12.04 % Favored : 87.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.65 (0.36), residues: 622 helix: 2.72 (0.26), residues: 426 sheet: 0.79 (1.09), residues: 24 loop : -0.68 (0.52), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 155 HIS 0.004 0.001 HIS A 619 PHE 0.007 0.001 PHE A 193 TYR 0.010 0.001 TYR A 180 ARG 0.008 0.000 ARG A 492 Details of bonding type rmsd hydrogen bonds : bond 0.04113 ( 347) hydrogen bonds : angle 3.92071 ( 1011) covalent geometry : bond 0.00243 ( 5676) covalent geometry : angle 0.42155 ( 7628) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 46 time to evaluate : 0.581 Fit side-chains REVERT: A 28 ASP cc_start: 0.8059 (t0) cc_final: 0.7704 (t0) REVERT: A 104 GLU cc_start: 0.8477 (mt-10) cc_final: 0.8144 (tt0) REVERT: A 129 ARG cc_start: 0.8870 (mtt90) cc_final: 0.8636 (mtt90) REVERT: A 420 SER cc_start: 0.8059 (t) cc_final: 0.7630 (p) REVERT: A 454 ARG cc_start: 0.8080 (OUTLIER) cc_final: 0.7586 (mmt-90) REVERT: A 647 ARG cc_start: 0.7408 (tpt170) cc_final: 0.7007 (ttp80) outliers start: 5 outliers final: 2 residues processed: 49 average time/residue: 1.5377 time to fit residues: 78.6394 Evaluate side-chains 46 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 43 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 GLU Chi-restraints excluded: chain A residue 454 ARG Chi-restraints excluded: chain A residue 611 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 57 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 47 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 43 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 185 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.093709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.064865 restraints weight = 8176.023| |-----------------------------------------------------------------------------| r_work (start): 0.2718 rms_B_bonded: 2.00 r_work: 0.2542 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.2398 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8825 moved from start: 0.6328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 5676 Z= 0.204 Angle : 0.487 6.309 7628 Z= 0.266 Chirality : 0.040 0.157 812 Planarity : 0.004 0.038 930 Dihedral : 15.004 143.568 1098 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.11 % Allowed : 12.22 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.45 (0.36), residues: 622 helix: 2.56 (0.25), residues: 422 sheet: 0.76 (1.08), residues: 24 loop : -0.66 (0.52), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 155 HIS 0.006 0.001 HIS A 619 PHE 0.012 0.001 PHE A 193 TYR 0.015 0.001 TYR A 212 ARG 0.008 0.000 ARG A 492 Details of bonding type rmsd hydrogen bonds : bond 0.05029 ( 347) hydrogen bonds : angle 4.14171 ( 1011) covalent geometry : bond 0.00464 ( 5676) covalent geometry : angle 0.48738 ( 7628) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5777.10 seconds wall clock time: 101 minutes 17.38 seconds (6077.38 seconds total)